Variant ID: vg0322195173 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 22195173 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCGCCCACGCCGTGTCGAGCTCCGCCCGCTCCGCCTGCAGGGCCTCCATCTGGGCACTTAACCCGTCCAGCACCGTGCTGTTCGCGGCGGCCAAGGCCTG[T/C]
AGGAAGGGCTCCACGCTCAGTGGGGCAGCGGAAGACGTGCCGGACTCGGGGGCGTCCCTCGAAGCTGGCTCGTCCCAAGTGTCGCCCGAGGGGTCGGGCC
GGCCCGACCCCTCGGGCGACACTTGGGACGAGCCAGCTTCGAGGGACGCCCCCGAGTCCGGCACGTCTTCCGCTGCCCCACTGAGCGTGGAGCCCTTCCT[A/G]
CAGGCCTTGGCCGCCGCGAACAGCACGGTGCTGGACGGGTTAAGTGCCCAGATGGAGGCCCTGCAGGCGGAGCGGGCGGAGCTCGACACGGCGTGGGCGC
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 6.00% | 5.60% | 20.40% | 67.92% | NA |
All Indica | 2759 | 0.20% | 0.50% | 25.12% | 74.16% | NA |
All Japonica | 1512 | 18.10% | 16.30% | 9.72% | 55.89% | NA |
Aus | 269 | 0.00% | 0.00% | 35.69% | 64.31% | NA |
Indica I | 595 | 0.00% | 0.20% | 17.14% | 82.69% | NA |
Indica II | 465 | 0.00% | 0.60% | 6.67% | 92.69% | NA |
Indica III | 913 | 0.20% | 0.20% | 44.69% | 54.87% | NA |
Indica Intermediate | 786 | 0.40% | 1.10% | 19.34% | 79.13% | NA |
Temperate Japonica | 767 | 4.60% | 17.60% | 11.86% | 65.97% | NA |
Tropical Japonica | 504 | 43.10% | 13.10% | 7.34% | 36.51% | NA |
Japonica Intermediate | 241 | 8.70% | 19.10% | 7.88% | 64.32% | NA |
VI/Aromatic | 96 | 0.00% | 1.00% | 15.62% | 83.33% | NA |
Intermediate | 90 | 7.80% | 4.40% | 14.44% | 73.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0322195173 | T -> C | LOC_Os03g39930.1 | 5_prime_UTR_premature_start_codon_gain_variant ; LOW | silent_mutation | Average:14.149; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
vg0322195173 | T -> C | LOC_Os03g39930.1 | 5_prime_UTR_variant ; 52.0bp to feature; MODIFIER | silent_mutation | Average:14.149; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
vg0322195173 | T -> C | LOC_Os03g39920.1 | downstream_gene_variant ; 2003.0bp to feature; MODIFIER | silent_mutation | Average:14.149; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
vg0322195173 | T -> C | LOC_Os03g39940.1 | downstream_gene_variant ; 2722.0bp to feature; MODIFIER | silent_mutation | Average:14.149; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
vg0322195173 | T -> DEL | N | N | silent_mutation | Average:14.149; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |